Package picard.illumina.parser
Class BaseIlluminaDataProvider
- java.lang.Object
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- picard.illumina.parser.BaseIlluminaDataProvider
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- All Implemented Interfaces:
AutoCloseable
,Iterable<ClusterData>
,Iterator<ClusterData>
public abstract class BaseIlluminaDataProvider extends Object implements Iterator<ClusterData>, Iterable<ClusterData>, AutoCloseable
Parse various formats and versions of Illumina Basecall files, and use them the to populate ClusterData objects.
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Field Summary
Fields Modifier and Type Field Description static Pattern
FILE_NAME_PATTERN
protected int
lane
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Constructor Summary
Constructors Constructor Description BaseIlluminaDataProvider(int lane, OutputMapping outputMapping)
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Method Summary
All Methods Static Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description protected void
addData(ClusterData clusterData, picard.illumina.parser.BarcodeData barcodeData)
protected void
addData(ClusterData clusterData, picard.illumina.parser.PfData pfData)
protected void
addData(ClusterData clusterData, picard.illumina.parser.PositionalData posData)
protected void
addReadData(ClusterData clusterData, int numReads, picard.illumina.parser.BaseData baseData)
protected void
addReadData(ClusterData clusterData, int numReads, CbclData cbclData)
protected void
addReadData(ClusterData clusterData, int numReads, picard.illumina.parser.QualityData qualityData)
abstract void
close()
static Integer
fileToTile(String fileName)
Iterator<ClusterData>
iterator()
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Methods inherited from interface java.util.Iterator
forEachRemaining, hasNext, next, remove
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Field Detail
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FILE_NAME_PATTERN
public static final Pattern FILE_NAME_PATTERN
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lane
protected final int lane
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Constructor Detail
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BaseIlluminaDataProvider
public BaseIlluminaDataProvider(int lane, OutputMapping outputMapping)
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Method Detail
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iterator
public Iterator<ClusterData> iterator()
- Specified by:
iterator
in interfaceIterable<ClusterData>
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close
public abstract void close()
- Specified by:
close
in interfaceAutoCloseable
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addData
protected void addData(ClusterData clusterData, picard.illumina.parser.PositionalData posData)
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addData
protected void addData(ClusterData clusterData, picard.illumina.parser.PfData pfData)
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addData
protected void addData(ClusterData clusterData, picard.illumina.parser.BarcodeData barcodeData)
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addReadData
protected void addReadData(ClusterData clusterData, int numReads, picard.illumina.parser.BaseData baseData)
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addReadData
protected void addReadData(ClusterData clusterData, int numReads, picard.illumina.parser.QualityData qualityData)
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addReadData
protected void addReadData(ClusterData clusterData, int numReads, CbclData cbclData)
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